DNA in our Food? Extracting DNA from Strawberry. Teacher Guide

Transcription

1 DNA in our Food? Extracting DNA from Strawberry Teacher Guide Teacher Guide NGSS Alignment... T1 Unit Overview... T3 Teacher s Background... T4 Inventory Sheet... T4 Student Reading... T5 DNA in our Food? Extracting DNA from Strawberry Student Guide Introduction... 1 Getting Ready... 1 Lab Activity... 2 Vocabulary Knowledge Sheet... 4 Student Worksheet... 5 Supplementary Resources: See accompanying slides and other materials to help you teach this lesson at the BABEC website at If you have questions, please contact us at babec@babec.org. Version October 2017

2 NGSS Alignment Disciplinary Core Ideas Components that align to the transformation curriculum? (DCI) LS1: From Molecules to Organisms: Structures and Processes LS1.A Structure and function LS3: Heredity: Inheritance and Variation of Traits LS3.A Inheritance of traits LS3.B Variation of traits LS4: Biological Evolution: Unity and Diversity LS4.A Evidence of common ancestry and diversity LS4.D Biodiversity and humans All cells contain genetic information in the form of DNA molecules. Genes are regions in the DNA that contain the instructions that code for the formation of proteins, which carry out most of the work of cells. (PE: HS-LS1-1) The instructions for forming species characteristics are carried in DNA. All cells in an organism have the same genetic content, but the genes used (expressed) by the cell may be regulated in different ways. (PE: HS-LS3-1) Environmental factors also affect expression of traits, and hence affect the probability of occurrences of traits in a population. Thus the variation and distribution of traits observed depends on both genetic and environmental factors. (PE: HS-LS3-2) Genetic information provides evidence of evolution. DNA sequences vary among species, but there are many overlaps; in fact, the ongoing branching that produces multiple lines of descent can be inferred by comparing the DNA sequences of different organisms. (PE: LS4-1) Biodiversity is increased by the formation of new species (speciation) and decreased by the loss of species (extinction). Human activity is adversely impacting biodiversity. (PE: LS4-6) Science & Engineering Practices (SEP) 1. Asking Questions and Defining Problems 2. Developing and Using Models 3. Planning and Carrying Out Investigations 4. Analyzing and Interpreting Data 5. Using Mathematics and Computational Thinking 6. Constructing Explanations and Designing Solutions 7. Engaging in Argument from Evidence 8. Obtaining, Evaluating, and Communicating Information How does the Strawberry DNA Extraction Curriculum align? It asks empirically testable questions concerning how the process of extracting DNA can be done easily using everyday household items. Engage with a phenomenom: separating DNA from other molecules like carbohydrates, proteins, fats. Students observe DNA precipitation and write I notice I wonder. It creates opportunities for hands-on, iterative modeling of: cell membrane permeability, charge interactions between different components of the cell membrane and in the molecular structure of DNA. It follows a clear procedure, explains the purpose of the main steps in the protocol and allows the students to perform the experiment, make observations and make changes to the procedure to see how their investigation changes. Students can analyze the results by changing the conditions of extraction. Students are to use basic math to re-make the extraction buffer using a smaller scale. It provides tangible, empirical results. Students describe the importance of DNA extraction and how different organisms may require different methods of extraction. Students can predict what would happen if they omit a certain reagent from their extraction buffer, perform the experiment, make observations and conclude by providing the evidence from their observations. It has multiple opportunities for students to communicate basic scientific concepts: DNA structure & function, shared characteristics of organism, standard laboratory techniques, and ethical considerations to using human DNA for sequencing. Version October 2017 T1

3 Cross Cutting Concepts (CCC) 1. Patterns 2. Cause and Effect 3. Scale, Proportion, and Quantity 4. Systems and System Models 6. Structure and Function 7. Stability and Change How does the Strawberry DNA Extraction Curriculum align? DNA structures have a pattern. The structure of DNA does not change in any organism but the amount of DNA may change, or the DNA sequence may vary. Cells also consists of a pattern of organelles. By looking at just the cells, you may not be able to distinguish the origin of the cells. The addition of certain chemicals change the molecular interactions thereby allowing the distruption of cells or the DNA to precipiate out of solution. Changing the chemicals may change the outcome. In this expermental process, reagents are used at specific amount. If the amounts are omitted or were to increase or decrease, this may alter the results of the experiment. Cells are a system made of different components that have their own functions but interact to have cellular function. Cells and DNA have different types of structure: cellular and molecular. The interaction with other chemicals such as salt or detergent alters these structures. Cells are stable in certain environments. They can also change in certain environments. The addition of chemicals change the structure of the cells so they are no longer stable. Version October 2017 T2

4 Unit Overview This lesson is the first of the Getting Started series which includes DNA extraction, micro-pipetting and gel electrophoresis. This series introduces students to concepts and lab fundamentals that may prepare them to perform more advanced PCR labs including DNA extraction from their own cheek cells, insects (Wolbachia PCR) or food materials (GMO PCR) and setting up multiple types of PCR reactions. Furthermore, suggested activities follow different dimensions of NGSS. Suggestions for Background Learning Activities: Look at plant cells and identify the cell wall, cell membrane, cytoplasm and nucleus. Additional organelles can be studied. Using large cell model as manipulative, show the cell wall, cell membrane, cytoplasm and nucleus and DNA molecules. The nucleus is surrounded by the nuclear membrane (envelope), which protects the DNA molecules. DNA molecules code for proteins and are made of millions of atoms. Activity #1 DNA Vocabulary Review (refer to vocabulary knowledge worksheet on page 4) Activity #2 Reading with pictures (see page T5) 1. Allow the students to read the small paragraph and or use the graphics to understand each component that will be used in this experiment. 2. Revisit vocabulary knowledge worksheet by filling in the definitions Activity #3 I notice, I wonder 1. Show youtube video: 2. Students fill out I notice, I wonder on the Student Worksheet. Use some of the vocabulary from the Vocabulary Knowledge worksheet 3. Discuss what they are observing and what questions they may have Activity 4 DNA extraction protocol 1. Make the extraction buffer as a class demo (make enough for the whole class) 2. Direct instruction with I do then you do. Have students follow protocol as teacher does. 3. Make observations as the procedure is followed onto the Student Worksheet. 4. Explain or ask students to explain: a) Mashing the strawberries physically breaks-down the strawberry b) Adding the extraction buffer makes chemical changes c) The soap dissolves the lipid-rich cell membranes, allowing the DNA to leave the nucleus and cell d) The salt (NaCl) neutralizes the phosphate backbone and helps to neutralize and unravel the DNA e) The alcohol creates an interface with the strawberry and buffer solution, in which the DNA strands are precipitated into the alcohol Activity 5 Student Worksheet (see PowerPoint slides) Use this worksheet for observations and to answer questions. What do scientists do with the extracted DNA? Why extract DNA? What are they used for? Suggested Timeline for this activity: Optional Background Activity (50 min) Activity 1:DNA Vocabulary Knowledge Activity 2: Reading with Visuals to revise DNA Vocabulary Knowledge (50 min) Activity 3: Phenomenon with I notice/i wonder & Slide deck Activity 4: DNA extraction (50 min) Activity 5: Student Worksheet (HW) Version October 2017 T3

5 Teacher s Background DNA extraction is a fundamental procedure used in many types of experiment. It is a simple protocol so students are introduced to how to read protocols or procedures including the practice of reading ahead and following the procedures accurately. Extracting enough DNA onto a rod is a fun activity allowing students to see the DNA they isolate. In this activity, ripe strawberries are the source for DNA extraction. Strawberries range from being diploid to polyploid (up to 10 ploidy) so their DNA is abundant and easy to extract. Strawberries are also, by nature, very easy to squish and break down as they contain cellulase and pectinase that break down cell walls. Students get to try this experiment twice. The first time, students follow the protocol. The 2 nd time, they will omit one chemical from their extraction buffer to see if the extraction buffer still works with a missing component. Purpose of the reagents in this procedure: Shampoo or dish soap: Helps to dissolve the cell membrane, a lipid bilayer. Sodium Chloride (NaCl): A salt that dissociates to Na + and Cl -. The Na + surrounds the negative charge of the DNA phosphate backbone thereby neutralizing the charges and allowing the DNA to come out of solution or precipitate when alcohol is added. The salt also helps the proteins remain dissolved in the aqueous layer to prevent precipitation with the DNA. Ethanol or isopropyl alcohol: Allows the DNA to come out of solution. DNA will clump up, making it visible and easy to isolate on a stirring rod. Inventory Sheet: Listed below are the reagents and consumables provided in the DNA in our Food? Strawberry DNA extraction kit from BABEC, as well as additional reagents and consumables. Make sure also to read the list of equipment needed for this laboratory activity. For this activity, a team is considered a group of 4 students. The kit contains enough reagents for 40 students (10 teams), performing the experiment 2 times. Item Storage Amount Per Kit 91% Isopropanol (works best when very cold) Freezer (-20 C) 200mL 8mL Cheesecloth or Coffee Filter Room Temp (20 25ºC) 21 pieces 1 piece Test Tube/15ml Falcon Tube Room Temp (20 25ºC) 11 1 A bacterial loop, coffee stirrer or any type of rod Room Temp (20 25ºC) 21 1 Ziplock/Sandwich Bags Room Temp (20 25ºC) 25 2 bags Small Funnel Room Temp (20 25ºC) Plastic Cups or Beakers Room Temp (20 25ºC) Spoons Room Temp (20 25ºC) For Extraction Buffer NaCl or Table Salt (non-iodized) Room Temp (20 25ºC) 50 tsp 2 tsp Amount Per Team for performing the experiment twice Dish Soap Room Temp (20 25ºC) 200mL 10mL (2tsp) Reagents/Consumables NOT Provided in the BABEC Kit Item Storage Total needed Amount Per Team ½ or 1 strawberry Freezer (-20 C) thaw before Strawberries use or; Refrigerator (4 o (depends on the size of C) the strawberry Freezer (-20 C) thaw before Other fruit, like kiwi use or; Refrigerator (4 o 10 varies C) Version October 2017 T4

6 Students: Read the description below. Use the visuals to help you understand how each component of the DNA extraction works. Extracting DNA from a plant cell or an animal cell is an easy process. The items you need are: soap or detergent, salt and alcohol. Cells are made of lipids or fats. Detergents are great at lysing or disrupting the cell and nuclear membranes of each cell to release the DNA. DNA is a large molecule that is negatively charged. Salt can be sodium chloride or NaCl. When dissolved in water, the NaCl will come apart to become so positive ions (Na + ) or negative ions (Cl - ). The positive ions (Na + ) surrounds the DNA to neutralize the negative charge. Alcohol then pulls the water away from the DNA (while dissolving the other components like proteins and fats) to precipitate or allow the DNA to come out of solution. You can see the clumps of DNA from this experiment! Detergents work via polar interactions Salt: Positive and negative charges cancel each other out. DNA is now neutral DNA How do detergents disrupt cells? Add detergent Membrane breaks apart, cell lysis and DNA can come out Version October 2017 T5

7 DNA in our Food? Extracting DNA from Strawberry Student Guide Introduction: DNA extraction is a fundamental procedure used in a lab that is simple and effective. Extracting enough DNA to spool onto a rod is a fun activity allowing students to see the DNA they isolate. In this activity, ripe strawberries are the source for DNA extraction. Strawberries range from being diploid to polyploid (up to 10 ploidy that means lots of copies of chromosomes) so their DNA is easy to extract. Strawberries are also, by nature, very easy to squish and break down as they contain cellulase and pectinase that break down cell walls. Learning objectives: 1. Understand the process of DNA extraction; why certain chemicals are used to obtain nuclear DNA. 2. Observe the extracted DNA 3. Know different reasons to why scientists extract DNA from various organisms. 4. Learn how to read a procedure or protocol. 5. Steps to reading procedures: 1) Read through the whole procedure first; 2) ask clarifying questions; 3) follow procedure, and read ahead if there is down time! Getting Ready: The teacher may make the extraction buffer as a demonstration so students can see the reagents that go into the buffer. You will need For the extraction buffer: Items: A Cup Salt Dish soap Spoon For the activity: Items: A Ziploc Bag One Strawberry Extraction Buffer One Test Tube A Stirring Rod Alcohol Cheesecloth or Coffee Filter Funnel (if available) Extraction Buffer Version October

8 Name: Period: Step 1 DNA in our Food? Strawberry DNA Extraction Lab Activity Observe your teacher making the EXTRACTION BUFFER. In a plastic cup or beaker: 2 tsp of salt and 10ml of dish soap in 100ml of water (or ½ C of water) Mix by stirring Step 2 Remove any green leaves from the strawberries Remove the green parts. Step 3 Put the strawberry in a plastic bag and gently squish the strawberry with your fingers for 2 minutes What does the squishing do to the strawberry? Step 4 Add 10 ml of the Extraction Buffer to the bag, remove the air and close the bag What does the extraction do to the strawberry? 10mL Or use a medicine cup Step 5 Squeeze, massage and squish gently, mixing for 1 minute. Step 6 Pour the extract onto the cheesecloth in the funnel and let it drip into the beaker Squeeze to speed up the process 1 Why do you need to filter it through the cheesecloth? 2 (3 optional) Version October

9 Step 7 Add 4 ml filtered strawberry mush to a test tube, or about 1/4 full in the test tube. Step 8 Slowly add 4ml (or an equal volume) of alcohol down the side of the test tube. Let sit about 2 minutes while observing the interface between alcohol and strawberry solution. What happens when you add the alcohol? What do you notice? Slowly pour down side of the tube Step 9 Dip the rod into the tube at the interface between the alcohol and strawberry layers; begin spooling the DNA Interface: DNA Step 10 Store the DNA in a small tube filled with water Optional: Repeat your steps, but omit a reagent when making your extraction buffer or change the amount of salt, detergent, alcohol used. Use math to proportion out your reagent to make 10mL. Last Step Put away items, clean up area and wash hands. Version October

10 DNA in our Food? Vocabulary Knowledge Rating Name: Period: Date: Vocabulary Knowledge Rating: For each term, please mark your level of familiarity with a. Then provide a definition. Terms Know it. I can define this! Seen it. Maybe it means New to me. Totally guessing here. Definition in your own words Dissolve Salt Alcohol Attract/repel Positive/Negative charge Neutral charge Polar/non-polar Interface Lyse Charge of DNA Precipitate Cell membrane Nuclear membrane Version October

11 DNA in our Food? Extracting DNA from strawberries Student Worksheet Name: Period: Date: 1. Watch the video closely. Write down what you observed. I notice 2. Now, think of questions you have and write down what you wonder about. I wonder 3. Perform your experiment by following the procedures on pages 2-3, writing down your observations. 4. Observations: a. What did you observe after adding the extraction buffer & squishing? Did you notice bubbles? Do you see the plant cell walls breaking up? What is the consistency of the strawberry? b. What did your strawberry extraction look like after you filtered the big chunks out? c. What did you observe after you added the alcohol? Version October

12 d. What do you see on the stirring rod? What do you think other DNAs will look like? e. If you looked at the DNA under a microscope, explain how the DNA differs from cells. f. Are there other organisms you would like to isolate the DNA from? Why? g. How would the procedure differ, if any if you were to isolate DNA from other organisms? Why? 5. What do scientists do with the extracted DNA? What would you like to do with your own DNA? Version October

13 6. Now match the procedure with what it is doing to help isolate the DNA from the other materials in the cell. a. Squish the fruit to slush A. Break apart large plant cells to allow the extraction buffer to work. b. Mix in a detergent B. Precipitate the DNA (allow the DNA to clump together) c. Add the salt d. Filter your extract through cheesecloth e. Layer cold alcohol over the extract C. Separate large cell parts, broken cell wall and membranes from proteins, carbohydrates and DNA D. Neutralize the DNA so it has no charge E. Dissolve cell membranes Version October